On 05/28/2015 07:12 PM, David Leader wrote:
> I’m trying to prepare some figures for publication and I want to show
> hydrogen bonds between NH and O of backbone peptide bonds. If I use the
> command:
>
> restrict (118,119,120,121,122,123) AND NOT (*.H???, *.1H???, *.2H???, *.3H???)
> wireframe 0.3
>
> This selects the residues I want and their side chains but none of the
> hydrogens. The peptide bond hydrogens have names like [GLY]121:A.H #1721
> whereas the sidechain hydrogens have names like [GLN120]A.2HE2 #1705 .
> Is there an expression that will keep the Hs I want
>
> I’ve tried the alternative of finding the atom numbers of the Hs I want to
> visualise and selected them, but I can only visualise them by “spacefill” -
> “wireframe 0.3" does nothing after selection.
>
The default behaviour of Jmol is that both atoms of a bond must be
selected before 'wireframe 0.3' shows the bond.
There is a switch called 'bondModeOr' that influences this behaviour.
David, in your case you would need to set it to true:
set bondModeOr true
You could also use the (older) command "set bondmode OR". But the
advantage of the newer switch 'bondModeOr' is that you can query it's value:
if (bondModeOr) {
print "wireframe command works with one selected atom of a bond";
} else {
print "wireframe command works only with two selected atoms of a bond";
}
> Googling just adds to my woes. Is there a document anywhere that explains
> this dreadful scripting language?
>
You can find the documentation here:
http://www.stolaf.edu/academics/chemapps/jmol/docs/
It's not a tutorial but it explains a lot.
The documentation of the 'wireframe' command
("http://chemapps.stolaf.edu/jmol/docs/#wireframe";) explains for example
the older 'bondmode' switch. And there is a section on bond styles
("http://chemapps.stolaf.edu/jmol/docs/?ver=14.4#setbondstyles";) that
explains the older and the newer switches.
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
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